As quantum computers advance toward the regime of MegaQuOp machines executing millions of gates, a decoding system capable of real-time error correction in such a device will be crucial. Recent efforts have been focused on decoding an error-corrected
As quantum computers advance toward the regime of MegaQuOp machines executing millions of gates, a decoding system capable of real-time error correction in such a device will be crucial. Recent efforts have been focused on decoding an error-corrected memory or a small number of logical operations. Here we demonstrate an end-to-end real-time decoding stack for a universal fault-tolerant trapped-ion quantum computer architecture capable of decoding real workloads with millions of logical gates over hundreds of logical qubits. The complete pipeline, including on the fly detector error model generation, decoding of all logical qubits, logical operations, and magic-state factories, runs on a single CPU. We benchmark the decoder on practically relevant quantum applications spanning up to 408 logical qubits, and up to one million T gates. Assuming a trapped-ion architecture with 1 to 5 ms cycle time, the decoding delay stretches the computation by less than 0.3\% at p_{CNOT}=10^{-4} and less than 12\% at p_{CNOT}=5\times 10^{-4} for all workloads studied. These results demonstrate real-time decoding at MegaQuOp scale on a single conventional CPU.